# HG changeset patch
# User fubar
# Date 1371033055 14400
# Node ID 1eb7a4834c1ab370dd5c75d93e990092196b144d
# Parent  a4d7ec124c53f300b9168ba1144bdd65287831ed
Uploaded

diff -r a4d7ec124c53 -r 1eb7a4834c1a rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 06:17:03 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 06:30:55 2013 -0400
@@ -1,12 +1,15 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
+    </set_environment>
     <package name="package_BioCBasics" version="2.12">
         <install version="1.0">
             <actions>
                 <action type="set_environment_for_install">
                     <repository name="package_R3" owner="fubar" prior_installation_required="True"  toolshed="http://testtoolshed.g2.bx.psu.edu/"/>
                 </action>
-                <action type="shell_command">$R_HOME/bin/R CMD BATCH installBioC.R </action>
+                <action type="shell_command">$R3_BINARY/R CMD BATCH $R_SCRIPT_PATH/installBioC.R </action>
             </actions>
         </install>
         <readme>R is a free software environment for statistical computing and graphics